Initial version v0.1

This release creates a referenceable version of the single-cell RNA-seq preprocessing pipeline.

Features include:

• Automatic download of transcriptome reference(s) for mouse and human from Gencode.
• Streamed cleaning of fastq files using htstream.
• Expression quantification using salmon or kallisto (UMI-aware).
• Automatic creation of a SingleCellExperiment container for downstream analysis in R, with statistics from preprocessing.

Upcoming

Upcoming releases will implement the following features:

• Reformatting fastq header lines using the umis tool.
• Demultiplexing of fastq files using pydemult.
• S3 / Kubernetes support for cloud-based deployments.